Merge branch 'Cubix' into 'preprod'

New Cubix version, including Radwares utilities

See merge request !43

src/root/core/CMakeLists.txt

@@ -57,6 +57,21 @@ link_directories(${CMAKE_LIBRARY_OUTPUT_DIRECTORY})
 #
 # configure file
 #
+
+#TEST current configuration OS
+if ( UNIX )
+        set(CMAKE_OS_TYPE 1)
+endif()
+if ( WIN32 )
+        set(CMAKE_OS_TYPE 2)
+endif()
+if ( CYGWIN )
+        set(CMAKE_OS_TYPE 3)
+endif()
+if ( APPLE )
+        set(CMAKE_OS_TYPE 4)
+endif()
+
 configure_file (
     "${CMAKE_CURRENT_SOURCE_DIR}/GwConfig.h.cmake"
     "${CMAKE_BINARY_DIR}/include/GwConfig.h"

src/root/core/GwConfig.h.cmake

@@ -43,3 +43,14 @@
 #define GW_MacrosPath			"@GW_DATA_DIR@/macros";
 	
 #endif
+
+//////////////////////////////
+////// Define OS_TYPE ////////
+//////////////////////////////
+
+#define OS_LINUX   1
+#define OS_WINDOWS 2
+#define OS_CYGWIN  3      // rather useless ==> to be removed ??
+#define OS_APPLE   4
+
+#define OS_TYPE @CMAKE_OS_TYPE@

src/root/gui/cubix/CMakeLists.txt

@@ -38,7 +38,7 @@ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -pthread -Wno-unused-paramete
 # root
 INCLUDE_DIRECTORIES( ${ROOT_INCLUDE_DIR} )
 LINK_DIRECTORIES( ${ROOT_LIBRARY_DIR} )
-SET(EXTRA_EXTERNAL_LIBRARIES ${EXTRA_EXTERNAL_LIBRARIES} Matrix)
+SET(EXTRA_EXTERNAL_LIBRARIES ${EXTRA_EXTERNAL_LIBRARIES} Matrix Rint)
 
 # gw
 set(EXTRA_INTERNAL_LIBRARIES GWPHYSICS )

src/root/gui/cubix/Root2Rad/Conf/Calib.aca

+  ENCAL OUTPUT FILE
+ TMEUHS.STO          EU152.SOU           TM 159 EU152 HIGH SPIN CALIBRATION      
+    2 0.000000000000D+00 1.000000000000D+00 0.000000000000D+00
+      0.000000000000D+00 0.000000000000D+00 0.000000000000D+00

src/root/gui/cubix/Root2Rad/Conf/Cube.conf

+### Cube file
+CubeFileName MyCube.cub
+
+### 2D projection file
+2DProj MyCube.2dp
+
+### LUT file
+LUT MyCube.tab
+
+### Contraction factor (default 1)
+CompressFact 1
+
+### Total projection file
+TotalProj MyCube.spe
+
+### Backgroud file
+BackgroudFile MyCubeBG.spe
+
+### Calibration file (not mandatory)
+#CalFile MyCube.aca
+
+### Efficiency file (not mandatory)
+#EffFile MyCube.aef

src/root/gui/cubix/Root2Rad/Conf/CubeBuilder.conf

+#######################
+### Cube Properties ###
+#######################
+
+# Name of the 3D cube file
+CubeFileName MyCube.cub
+# name of the look-up table file to be used to map ADC chs to cube chs
+TabFile test.tab
+# Size to be used for the "scratch" disk file, in MB
+ScratchSize 512
+# Compression factor (to obtain binning <1 keV, one needs to scale the energy)
+# For example, to obtain a minimal 0.5 KeV/Channel, we fill the Cube on 8k channel for 4keV range ==> Compression factor = 2
+# Must be similar to the value in the GenBinning conf file
+CompressionFactor 1
+
+################################
+## Input Root Tree Properties ##
+################################
+
+#Name of the input TTree (regular expressions can be used as for building TChain)
+TreeFile MyTree.root
+
+#Name of the TTree
+TreeName TreeName
+
+#Events to process (0 => All)
+NEvents 1000
+
+#Name of the branch corresponding to the gamma-ray energy
+EGamma EGamma
+
+#Name of the branch corresponding to the gamma-ray muliplicity
+GammaMult GammaMult
+
+#Cut to be apllied (see TTreeFormulaExpression)
+Cut None

src/root/gui/cubix/Root2Rad/Conf/Efficiency.aef

+ EFFIT PARAMETER FILE  19-FEB-92 10:14:04
+ 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
+ 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+02 0.00000000E+03

src/root/gui/cubix/Root2Rad/Conf/GenBinning.conf

+#Name of the tab file
+TabFile test.tab
+
+#To fit the FWHM vs Energy function:
+#Fit function: sqrt([0]*[0] + [1]*[1]*x/1000. + [2]*[2]*x/1000.*x/1000.)
+#For each new point: FWHM   Energy (keV)   Value (keV)
+FWHM   122.   1.35
+FWHM   1333.  2.35
+FWHM   2500.  3.00
+
+# Compression factor (to obtain binning <1 keV, one needs to scale the energy)
+# For example, to obtain a minimal 0.5 KeV/Channel, we fill the Cube on 8k channel for 4keV range ==> Compression factor = 2
+CompressionFactor 1
+
+#Number of bin per FWHM
+Precision 1
+
+#RangeMax (keV)
+RangeMax 8192

src/root/gui/cubix/Root2Rad/Makefile

+ROOTCFLAGS   := $(shell root-config --cflags)  
+ROOTLIBS     := $(shell root-config --libs)
+
+CXX      = g++
+CXXFLAGS = -O3 -I . -w
+
+CXXFLAGS = -O3 -I ./src -w -g $(ROOTCFLAGS) -Wno-write-strings -Wno-unused-result
+LDFLAGS = ${ROOTLIBS}
+
+obj_CubeBuilder = src/CubeBuilder.o src/progressbar.o 
+obj_GenBinning = src/GenBinning.o src/util.o 
+
+ALL = CubeBuilder GenBinning
+
+.PHONY: all
+all: $(ALL)
+
+CubeBuilder: $(obj_CubeBuilder)
+	$(CXX) $^ -o $@ $(LDFLAGS) $(CXXFLAGS)
+	
+GenBinning: $(obj_GenBinning)
+	$(CXX) $^ -o $@	$(LDFLAGS) $(CXXFLAGS)
+
+.PHONY: clean
+clean:
+	rm -f $(ALL) src/*.o 

src/root/gui/cubix/Root2Rad/ReadMe_CubeBuilder.txt

+ReadMe CubeBuilder:
+
+1 - Generate the adaptative binning file:
+
+./GenBinning ConfBinning.txt
+This will produce:
+- The binning file: Binning.tab
+- A width spectrum file: Binning.spe
+
+
+2 - Generate the Cube
+
+./CubeBuilder ConfBuildCube.conf
+This will produce:
+- The cube file: MyCube.cub
+
+3 - Generate the total projection
+
+(radware prog) pro3d => MyCube.cub
+This will produce:
+- The total 2D projection spectrum: MyCube.2dp
+- The total 1D projection spectrum: MyCube.spe
+
+4 - Generate the background (in gf3)
+
+in gf3:
+
+4-1: Open the 1D projection: MyCube.spe
+4-2: Divide by the width spectrum: DV, then Binning.spe
+4-3: Calculate background: BG, then ok, then click limits on the graph
+4-4: Multiply by the width spectrum: MS, then Binning.spe
+4-5: Save the background spectrum: WS, then file name

src/root/gui/cubix/Root2Rad/src/CubeBuilder.h

+
+#define RW_MAXFILES 9999         /* Max files per tape to read */
+#define RW_MAXRECORDS 1000000000 /* Max number of records per tape to read */
+#define RW_DATFILE "incub8r.inc" /* Defaults file for hypercube */
+
+#define RW_CHNK_S  32      /* size of update chunk, in units of 1/4 MB      */
+
+/*
+   RW_LB2 = ceil((float)(ceil((float)((RW_MAXCH/8)*((RW_MAXCH/8)+1)*((RW_MAXCH/8)+2)/6)/128))/RW_CHNK_S)
+   RW_LB1 = RW_LB2*RW_CHNK_S
+*/
+
+//for 1400 channels
+
+//#define RW_MAXCH 1400            /* Maximum channels on cube axis */
+//                                 /*    (must be multiple of 8)    */
+//#define RW_LB2 222         /* length required for buf2, depends on RW_LB1   */
+//                           /* RW_LB2 >= RW_LB1/RW_CHNK_S                    */
+//#define RW_LB1 7104        /* length required for buf1, depends on RW_MAXCH */
+//                           /* RW_LB1 > x(x+1)(x+2)/(6*128),                 */
+//		                     /* where x = RW_MAXCH/8                          */
+//                           /* must also be a multiple of RW_CHNK_S          */
+
+//for 4096channels
+
+//#define RW_MAXCH 4096
+
+//#define RW_LB1 175808
+
+
+
+//#define RW_LB2 5494
+
+
+//for 8196 channels
+
+#define RW_MAXCH 8192
+
+#define RW_LB1 1402208
+
+#define RW_LB2 43819
+
+
+
+
+
+
+
+
+#define RW_DB1 90          /* depth of buf1 */
+
+#define RW_DB2 180         /* depth of buf2 not to exceed RW_SCR_RECL       */
+                           /* byte records in scr file                      */
+#define RW_SCR_RECL 32768  /* Record length of scr file                     */
+                           /* must be >= RW_DB2*2*(RW_DB1+1) + 4            */
+#define RW_MAXMULT 40
+
+
+/************************************************
+ *  3D CUBE FILE FORMAT
+ *  1024byte file header
+ *  4096byte data records
+ *
+ *      each data record contains:
+ *      variable number of bit-compressed 8x8x4 mini-cubes
+ *      8bytes header, 4088 bytes of data
+ */
+
+  /* 3d cube file header */
+typedef struct {
+  char id[16];            /* "Incub8r3/Pro4d  " */
+  int  numch;             /* number of channels on axis */
+  int  bpc;               /* bytes per channel, = 4 */
+  int  cps;               /* 1/cps symmetry compression, = 6 */
+  int  numrecs;           /* number of 4kB data records in the file */
+  char resv[992];         /* FUTURE flags */
+} FHead3D;
+
+  /* 3Drecord header */
+typedef struct {
+  int minmc;          /* start minicube number, starts at 0 */
+  short nummc;        /* number of minicubes stored in here */
+  short offset;       /* offset in bytes to first full minicube */
+} RHead3D;
+
+typedef struct {
+  RHead3D h;
+  unsigned char d[4088];  /* the bit compressed data */
+} Record3D;               /* see the compression alg for details */

src/root/gui/cubix/Root2Rad/src/GenBinning.cpp

+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <math.h>
+#include <string.h>
+#include <fstream>
+
+#include "util.h"
+
+#include "TGraph.h"
+#include "TF1.h"
+#include "TString.h"
+#include "TCanvas.h"
+#include "TApplication.h"
+#include "TSystem.h"
+
+using namespace std;
+
+float wid_spec[16384];
+float wa = 3.0f, wb = 1.0f, wc = 4.0f, cfactor = 1.0f, chs = 2.0f;
+float w, x, f1, f2, f3,  wa2, wb2, wc2;
+int   iclo = 200, ichi = 5000;
+int   i1, i2, i3, hi, lo, nc, i, j, ich2;
+int   nclook, lookmin, lookmax, rl = 0;
+short looktab[16384];
+char  buf[32];
+TString TabName = "FWHM.tab";
+
+Bool_t fFixedBinning = false;
+
+bool CalcFWHMParameters(vector< pair<float,float> > calibpoints) {
+
+    TApplication *theApp = new TApplication("App", 0, 0);
+
+    TGraph *CalibGraph = new TGraph;
+    CalibGraph->SetNameTitle("CalibFWHM","CalibFWHM");
+
+    TF1 *CalibFunc = new TF1("CalibFunc","sqrt([0]*[0] + [1]*[1]*x/1000. + [2]*[2]*x/1000.*x/1000.)");
+
+    for(uint i=0 ; i<calibpoints.size() ; i++) {
+        CalibGraph->SetPoint(CalibGraph->GetN(),calibpoints.at(i).first,calibpoints.at(i).second);
+    }
+
+    TCanvas *c = new TCanvas;
+
+    CalibGraph->SetMarkerStyle(20);
+    CalibGraph->SetMarkerSize(2);
+    CalibGraph->SetMarkerColor(kBlue);
+    CalibGraph->Draw("APL");
+
+    CalibGraph->Fit(CalibFunc,"SQ");
+
+    wa2 = CalibFunc->GetParameter(0)*CalibFunc->GetParameter(0);
+    wb2 = CalibFunc->GetParameter(1)*CalibFunc->GetParameter(1);
+    wc2 = CalibFunc->GetParameter(2)*CalibFunc->GetParameter(2);
+
+    cout<<" -- Fit Function: FWHM = sqrt(F*F + G*G*x + H*H*x*x)  (x = ch.no. /1000)"<<endl;
+    cout<<"  --> F = "<< CalibFunc->GetParameter(0)<<endl;
+    cout<<"  --> G = "<< CalibFunc->GetParameter(1)<<endl;
+    cout<<"  --> H = "<< CalibFunc->GetParameter(2)<<endl;
+
+    c->Update();
+    c->Modified();
+    gSystem->Sleep(200);
+
+    gSystem->ProcessEvents();
+    gSystem->DispatchOneEvent(true);
+
+    bool ok = askyn("Agree with the fit ? (Y/N)");
+
+    delete theApp;
+
+    return ok;
+}
+
+int main(int argnc, char **argv)
+{
+
+  FILE  *tabfile = nullptr;
+
+  cout<<" -- This program is used to create lookup tables for incub8r and 4play replay tasks"<<endl;
+  cout<<"    Incub8r and 4play allow non-linear gains"<<endl;
+  cout<<"    This is an adaptation of the lufwhm program of the Radware package"<<endl;
+
+  if(argnc != 2)
+  {
+      cout<<" -- To generate a binning file, use the command: ./gen_binning Conf_binning.txt"<<endl;
+      cout<<"  --> see an example of conf file in conf/Conf_binning.txt"<<endl;
+      return 1;
+  }
+
+  vector< pair<float,float> > calibpoints;
+  pair<int, int> Range(0,8191);
+  Float_t NumberOfChannelPerFWHM = 1;
+  string line;
+  TString Buffer;
+
+  ifstream FileConf;
+  FileConf.open(argv[1], std::ifstream::in);
+
+  if(!FileConf) {
+      cout<<"No binning conf file ==> Exit"<<endl;
+      return 1;
+  }
+  int linenb=0;
+  while(FileConf) {
+      getline(FileConf,line);
+      linenb++;
+      Buffer = line;
+
+      TObjArray *loa=Buffer.ReplaceAll("\t"," ").Tokenize(" ");
+
+      if(Buffer.BeginsWith("#") || Buffer.Length()==0 ) continue;
+      if(Buffer.BeginsWith("TabFile")) {
+          if(loa->GetEntries() != 2) {
+              cout<<"Bad entry at line "<<linenb<<" ; skipped"<<endl; continue;
+          }
+          TabName = loa->At(1)->GetName();
+          if(!TabName.EndsWith(".tab")) TabName.Append(".tab");
+      }
+      if(Buffer.BeginsWith("FWHM")) {
+          if(loa->GetEntries() != 3) {
+              cout<<"Bad entry at line "<<linenb<<" ; skipped"<<endl; continue;
+          }
+          pair<float,float> value (((TString)loa->At(1)->GetName()).Atof(),((TString)loa->At(2)->GetName()).Atof());
+          calibpoints.push_back(value);
+      }
+      if(Buffer.BeginsWith("Precision")) {
+          if(loa->GetEntries() != 2) {
+              cout<<"Bad entry at line "<<linenb<<" ; skipped"<<endl; continue;
+          }
+          NumberOfChannelPerFWHM = ((TString)loa->At(1)->GetName()).Atof();
+      }
+      if(Buffer.BeginsWith("CompressionFactor")) {
+          if(loa->GetEntries() != 2) {
+              cout<<"Bad entry at line "<<linenb<<" ; skipped"<<endl; continue;
+          }
+          cfactor = ((TString)loa->At(1)->GetName()).Atof();
+      }
+      if(Buffer.BeginsWith("RangeMax")) {
+          if(loa->GetEntries() != 2) {
+              cout<<"Bad entry at line "<<linenb<<" ; skipped"<<endl; continue;
+          }
+          Range.first = 0;
+          Range.second = ((TString)loa->At(1)->GetName()).Atoi();
+      }
+      if(Buffer.BeginsWith("FixedBinning")) {
+          fFixedBinning = true;
+      }
+
+      delete loa;
+  }
+
+  tabfile = open_new_file(((char*)TabName.Data()), 1);
+  cout<<"Output tab file: "<<TabName.Data()<<endl;
+
+  chs = NumberOfChannelPerFWHM;
+
+  iclo = Range.first;
+  ichi = Range.second*cfactor;
+  cout<<" *-* "<<chs<<" channels per FWHM"<<endl;
+  cout<<" *-* Compression factor: "<<cfactor<<endl;
+  cout<<" *-* Channels Range: "<<iclo<<" -- "<<ichi<<endl;
+
+  if(fFixedBinning) {
+      cout<<" *-* Fixed binning used"<<endl;
+      wa2=1.;
+      wb2=0.;
+      wc2=0.;
+  }
+  else if(CalcFWHMParameters(calibpoints) == false)
+      return 1;
+
+  lo = iclo;
+  ich2 = 0;
+  while (lo <= ichi) {
+    ++ich2;
+    x = ((float) lo + 0.5f) / 1e3f;
+    w = sqrt(wa2 + wb2 * x/cfactor + wc2 * x/cfactor * x/cfactor) * cfactor;
+    int incr = (int) ((w / chs) + 0.5);
+    if(incr==0) incr = 1;
+    lo += incr;
+  }
+  if (!askyn("No. of chs. in cube = %d --- Okay? (Y/N)", ich2))
+      return 1;
+
+  nclook = ichi+1;
+
+  for (j = 0; j < nclook; ++j) {
+    looktab[j] = 0;
+  }
+  lo = iclo;
+  for (i = 1; i < ich2+1; ++i) {
+    x = ((float) lo + 0.5f) / 1e3f;
+    w = sqrt(wa2 + wb2 * x/cfactor + wc2 * x/cfactor * x/cfactor) * cfactor;
+    hi = lo + (int) ((w / chs) + 0.5);
+    if (hi > nclook) hi = nclook;
+    for (j = lo; j < hi; ++j) {
+      looktab[j] = i;
+    }
+    wid_spec[i - 1] = (float) (hi - lo)/cfactor;
+    if ((lo = hi) == nclook) break;
+  }
+
+  /* write out look-up table to disk file */
+  lookmin = 1;
+  lookmax = ich2;
+  rewind(tabfile);
+#define W(a,b) { memcpy(buf + rl, a, b); rl += b; }
+  W(&nclook, 4);
+  W(&lookmin, 4);
+  W(&lookmax, 4);
+#undef W
+  if (put_file_rec(tabfile, buf, rl) ||
+      put_file_rec(tabfile, looktab, 2*nclook)) {
+    file_error("write to", ((char*)TabName.Data()));
+    return 1;
+  }
+  fclose(tabfile);
+
+  TString SpectrumFileName = TabName.Copy().Append(".spe");
+  tell("The \"Width Spectrum\" has %d channels, and contains the width (in ADC-chs) for each cube channel.\n", ich2);
+  wspec((char*)SpectrumFileName.Data(), wid_spec, ich2);
+  tell("=> Width Spectrum written as file %s\n", SpectrumFileName.Data());
+
+  return 0;
+}

src/root/gui/cubix/Root2Rad/src/compress3d.cpp

+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+
+
+int
+compress3d (unsigned int *in, unsigned char *out)
+{
+  static int sum_limits[] = { 16,32,64,128,
+                  256,512,1024,2048,
+                  4096,8192,17000,35000,
+                  80000,160000,320000,640000 };
+
+  static int bitmask[] = { 0,1,3,7,15,31,63,127,255,511,1023,2047,
+               4095,8191,16383,32767 };
+  int cube_length;
+  int sum=0, i, j;
+  int nplanes, noverflows, stmp, nbits;
+  unsigned char *bitptr, *ovrptr;
+  int test1, test2, test3;
+
+  /* guess at depth of bit field */
+  for (i=0;i<256;i+=16) {
+    sum += in[i];
+  }
+
+  i = 7;
+  j = 8;
+  while (j>1) {
+    j = j / 2;
+    if (sum > sum_limits[i])
+      i += j;
+    else
+      i -= j;
+  }
+  if (sum > sum_limits[i+1])
+    nplanes = i + 1;
+  else
+    nplanes = i;
+
+  while (1) {
+    test1 = test2 = test3 = 0;
+    for (i=0;i<256;i++) {
+      test1 += in[i] >> nplanes;
+      test2 += in[i] >> (nplanes+1);
+      test3 += in[i] >> (nplanes+2);
+    }
+    if (test2 > 31) {
+      if (test3 > 31) {
+	nplanes += 3;
+	continue;
+      }
+      nplanes += 2;
+      noverflows = test3;
+      break;
+    }
+    else if (test1 > 31) {
+      nplanes += 1;
+      noverflows = test2;
+      break;
+    }
+    noverflows = test1;
+    break;
+  }
+
+  if (nplanes > 30)
+    fprintf(stderr,"Expecting core dump...\n");
+
+  /* insert length of compressed cube */
+  if (nplanes < 7) {
+    out[0] = 32*nplanes + noverflows;
+    bitptr = out+1;
+    cube_length = 1;
+  }